CURRENT ADVANCES

Recent advances in CRISPR research

  • Baohui Chen 1 ,
  • Yuyu Niu 2 ,
  • Haoyi Wang 3 ,
  • Kejian Wang 4 ,
  • Hui Yang 5 ,
  • Wei Li , 3
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  • 1. Department of Cell Biology, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
  • 2. Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650500, China
  • 3. State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
  • 4. State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
  • 5. Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Research Center for Brain Science and Brain-Inspired Intelligence, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China

Published date: 15 Nov 2020

Copyright

2020 The Author(s)

Cite this article

Baohui Chen , Yuyu Niu , Haoyi Wang , Kejian Wang , Hui Yang , Wei Li . Recent advances in CRISPR research[J]. Protein & Cell, 2020 , 11(11) : 786 -791 . DOI: 10.1007/s13238-020-00704-y

1
Abudayyeh OO, Gootenberg JS, Essletzbichler P, Han S, Joung J, Belanto JJ, Verdine V, Cox DBT, Kellner MJ, Regev A (2017) RNA targeting with CRISPR-Cas13. Nature 550:280–284

DOI

2
Abudayyeh OO, Gootenberg JS, Franklin B, Koob J, Kellner MJ, Ladha A, Joung J, Kirchgatterer P, Cox DBT, Zhang F (2019) A cytosine deaminase for programmable single-base RNA editing. Science 365:382–386

DOI

3
Allergan (2019) Single ascending dose study in participants with LCA10. ClinicalTrial.gov Identifier: NCT03872479. (clinicaltrials.-gov/ct2/show/NCT03872479)

4
Amoasii L, Hildyard JCW, Li H, Sanchez-Ortiz E, Mireault A, Caballero D, Harron R, Stathopoulou TR, Massey C, Shelton JM (2018) Gene editing restores dystrophin expression in a canine model of Duchenne muscular dystrophy. Science 362:86–91

DOI

5
Anzalone AV, Randolph PB, Davis JR, Sousa AA, Koblan LW, Levy JM, Chen PJ, Wilson C, Newby GA, Raguram A (2019) Search-and-replace genome editing without double-strand breaks or donor DNA. Nature 576:149–157

DOI

6
Cameron P, Coons MM, Klompe SE, Lied AM, Smith SC, Vidal B, Donohoue PD, Rotstein T, Kohrs BW, Nyer DB (2019) Harnessing type I CRISPR-Cas systems for genome engineering in human cells. Nat Biotechnol 37(12):1471–1477

DOI

7
Chen B, Gilbert LA, Cimini BA, Schnitzbauer J, Zhang W, Li GW, Park J, Blackburn EH, Weissman JS, Qi LS (2013) Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system. Cell 155:1479–1491

DOI

8
Chen B, Guan J, Huang B (2016a) Imaging Specific genomic DNA in living cells. Annu Rev Biophys 45:1–23

DOI

9
Chen B, Hu J, Almeida R, Liu H, Balakrishnan S, Covill-Cooke C, Lim WA, Huang B (2016b) Expanding the CRISPR imaging toolset with Staphylococcus aureus Cas9 for simultaneous imaging of multiple genomic loci. Nucleic Acids Res 44:e75

DOI

10
Chen B, Zou W, Xu H, Liang Y, Huang B (2018) Efficient labeling and imaging of protein-coding genes in living cells using CRISPRTag. Nat Commun 9:5065

DOI

11
Cheng AW, Jillette N, Lee P, Plaskon D, Fujiwara Y, Wang W, Taghbalout A, Wang H (2016) Casilio: a versatile CRISPR-Cas9Pumilio hybrid for gene regulation and genomic labeling. Cell Res 26:254–257

DOI

12
Chinese PLA General Hospital (2018) Study of PD-1 gene-knocked out mesothelin-directed CAR-T cells with the conditioning of PC in mesothelin positive multiple solid tumors. Identifier: NCT03747965.

13
Dolan AE, Hou Z, Xiao Y, Gramelspacher MJ, Heo J, Howden SE, Freddolino PL, Ke A, Zhang Y (2019) Introducing a spectrum of long-range genomic deletions in human embryonic stem cells using type I CRISPR-Cas. Mol Cell 74(5):936–950

DOI

14
Dreissig S, Schiml S, Schindele P, Weiss O, Rutten T, Schubert V, Gladilin E, Mette MF, Puchta H, Houben A (2017) Live-cell CRISPR imaging in plants reveals dynamic telomere movements. Plant J 91:565–573

DOI

15
Duan J, Lu G, Hong Y, Hu Q, Mai X, Guo J, Si X, Wang F, Zhang Y (2018) Live imaging and tracking of genome regions in CRISPR/ dCas9 knock-in mice. Genome Biol 19:192

DOI

16
Edraki A, Mir A, Ibraheim R, Gainetdinov I, Yoon Y, Song CQ, Cao Y, Gallant J, Xue W, Rivera-Perez JA (2018) A compact, highaccuracy Cas9 with a dinucleotide PAM for in vivo genome editing. Mol Cell 73(4):714–726

DOI

17
Fu Y, Rocha PP, Luo VM, Raviram R, Deng Y, Mazzoni EO, Skok JA (2016) CRISPR-dCas9 and sgRNA scaffolds enable dual-colour live imaging of satellite sequences and repeat-enriched individual loci. Nat Commun 7:11707

DOI

18
Gao X, Tao Y, Lamas V, Huang M, Yeh WH, Pan B, Hu YJ, Hu JH, Thompson DB, Shu Y (2018) Treatment of autosomal dominant hearing loss by in vivo delivery of genome editing agents. Nature 553:217–221

DOI

19
Gaudelli NM, Komor AC, Rees HA, Packer MS, Badran AH, Bryson DI, Liu DR (2017) Programmable base editing of A*T to G*C in genomic DNA without DNA cleavage. Nature 551:464–471

DOI

20
Grünewald J, Zhou R, Iyer S, Lareau CA, Garcia SP, Aryee MJ, Keith Joung J (2019) CRISPR adenine and cytosine base editors with reduced RNA off-target activities. bioRxiv. https://doi.org/10.1101/631721

DOI

21
Gu B, Swigut T, Spencley A, Bauer MR, Chung M, Meyer T, Wysocka J (2018) Transcription-coupled changes in nuclear mobility of mammalian cis-regulatory elements. Science 359:1050–1055

DOI

22
Han D, Hong Y, Mai X, Hu Q, Lu G, Duan J, Xu J, Si X, Zhang Y (2019) Systematical study of the mechanistic factors regulating genome dynamics in vivo by CRISPRsie. J Mol Cell Biol 11:1018–1020

DOI

23
Jin S, Zong Y, Gao Q, Zhu Z, Wang Y, Qin P, Liang C, Wang D, Qiu JL, Zhang F (2019) Cytosine, but not adenine, base editors induce genome-wide off-target mutations in rice. Science 364:292–295

DOI

24
Karvelis T, Bigelyte G, Young JK, Hou Z, Zedaveinyte R, Pociute K, Silanskas A, Venclovas Č, Siksnys V (2019) PAM recognition by miniature CRISPR-Cas14 triggers programmable doublestranded DNA cleavage. bioRxiv. https://doi.org/10.1101/654897

DOI

25
Kelliher T, Starr D, Su X, Tang G, Chen Z, Carter J, Wittich PE, Dong S, Green J, Burch E (2019) One-step genome editing of elite crop germplasm during haploid induction. Nat Biotechnol 37:287–292

DOI

26
Khanday I, Skinner D, Yang B, Mercier R, Sundaresan V (2019) A male-expressed rice embryogenic trigger redirected for asexual propagation through seeds. Nature 565:91–95

DOI

27
Kim D, Lim K, Kim ST, Yoon SH, Kim K, Ryu SM, Kim JS (2017) Genome-wide target specificities of CRISPR RNA-guided programmable deaminases. Nat Biotechnol 35:475–480

DOI

28
Klompe SE, Vo PLH, Halpin-Healy TS, Sternberg SH (2019) Transposon-encoded CRISPR-Cas systems direct RNA-guided DNA integration. Nature 571:219–225

DOI

29
Knight SC, Xie L, Deng W, Guglielmi B, Witkowsky LB, Bosanac L, Zhang ET, El Beheiry M, Masson JB, Dahan M (2015) Dynamics of CRISPR-Cas9 genome interrogation in living cells. Science 350:823–826

DOI

30
Knight SC, Tjian R, Doudna JA (2018) Genomes in focus: development and applications of CRISPR-Cas9 imaging technologies. Angew Chem Int Ed Engl 57:4329–4337

DOI

31
Komor AC, Kim YB, Packer MS, Zuris JA, Liu DR (2016) Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. Nature 533:420–424

DOI

32
Koonin EV, Makarova KS, Zhang F (2017) Diversity, classification and evolution of CRISPR-Cas systems. Curr Opin Microbiol 37:67–78

DOI

33
Kwon C-T, Heo J, Lemmon ZH, Capua Y, Hutton SF, Van Eck J, Park SJ, Lippman ZB (2019) Rapid customization of Solanaceae fruit crops for urban agriculture. Nat Biotechnol 38:182–188

DOI

34
Liu Z, Cai Y, Wang Y, Nie Y, Zhang C, Xu Y, Zhang X, Lu Y, Wang Z, Poo M (2018) Cloning of macaque monkeys by somatic cell nuclear transfer. Cell 172(881–887):e887

DOI

35
Liu C, Zhong Y, Qi X, Chen M, Liu Z, Chen C, Tian X, Li J, Jiao Y, Wang D (2019a) Extension of the in vivo haploid induction system from diploid maize to hexaploid wheat. Plant Biotechnol J 18:316–318

DOI

36
Liu J-J, Orlova N, Oakes BL, Ma E, Spinner HB, Baney KLM, Chuck J, Tan D, Knott GJ, Harrington LB (2019b) CasX enzymes comprise a distinct family of RNA-guided genome editors. Nature 566:218–223

DOI

37
Ma H, Tu LC, Naseri A, Huisman M, Zhang S, Grunwald D, Pederson T (2016a) CRISPR-Cas9 nuclear dynamics and target recognition in living cells. J Cell Biol 214:529–537

DOI

38
Ma H, Tu LC, Naseri A, Huisman M, Zhang S, Grunwald D, Pederson T (2016b) Multiplexed labeling of genomic loci with dCas9 and engineered sgRNAs using CRISPRainbow. Nat Biotechnol 34:528–530

DOI

39
Ma H, Tu LC, Naseri A, Chung YC, Grunwald D, Zhang S, Pederson T (2018) CRISPR-Sirius: RNA scaffolds for signal amplification in genome imaging. Nat Methods 15:928–931

DOI

40
Makarova KS, Wolf YI, Iranzo J, Shmakov SA, Alkhnbashi OS, Brouns SJJ, Charpentier E, Cheng D, Haft DH, Horvath P (2019) Evolutionary classification of CRISPR-Cas systems: a burst of class 2 and derived variants. Nat Rev Microbiol 18:67–83

DOI

41
Mao S, Ying Y, Wu X, Krueger CJ, Chen AK (2019) CRISPR/dualFRET molecular beacon for sensitive live-cell imaging of nonrepetitive genomic loci. Nucleic Acids Res 47:e131

DOI

42
Merkle T, Merz S, Reautschnig P, Blaha A, Li Q, Vogel P, Wettengel J, Li JB, Stafforst T (2019) Precise RNA editing by recruiting endogenous ADARs with antisense oligonucleotides. Nat Biotechnol 37:133–138

DOI

43
Morisaka H, Yoshimi K, Okuzaki Y, Gee P, Kunihiro Y, Sonpho E, Xu H, Sasakawa N, Naito Y, Nakada S (2019) CRISPR-Cas3 induces broad and unidirectional genome editing in human cells. Nat Commun 10:5302

DOI

44
Nelles DA, Fang MY, O’Connell MR, Xu JL, Markmiller SJ, Doudna JA, Yeo GW (2016) Programmable RNA Tracking in live cells with CRISPR/Cas9. Cell 165:488–496

DOI

45
Nelson CE, Wu Y, Gemberling MP, Oliver ML, Waller MA, Bohning JD, Robinson-Hamm JN, Bulaklak K, Castellanos Rivera RM, Collier JH (2019) Long-term evaluation of AAV-CRISPR genome editing for Duchenne muscular dystrophy. Nat Med 25:427–432

DOI

46
Qin P, Parlak M, Kuscu C, Bandaria J, Mir M, Szlachta K, Singh R, Darzacq X, Yildiz A, Adli M (2017) Live cell imaging of lowand non-repetitive chromosome loci using CRISPR-Cas9. Nat Commun 8:14725

DOI

47
Qiu PY, Jiang J, Liu Z, Cai YJ, Huang T, Wang Y, Liu QM, Nie YH, Liu F, Cheng JM (2019) BMAL1 knockout macaque monkeys display reduced sleep and psychiatric disorders. Natl Sci Rev 6:87–100

DOI

48
Qu L, Yi Z, Zhu S, Wang C, Cao Z, Zhou Z, Yuan P, Yu Y, Tian F, Liu Z (2019) Programmable RNA editing by recruiting endogenous ADAR using engineered RNAs. Nat Biotechnol 37:1059–1069

DOI

49
Rees HA, Liu DR (2018) Base editing: precision chemistry on the genome and transcriptome of living cells. Nat Rev Genet 19 (12):770–780

DOI

50
Shao S, Zhang W, Hu H, Xue B, Qin J, Sun C, Sun Y, Wei W, Sun Y (2016) Long-term dual-color tracking of genomic loci by modified sgRNAs of the CRISPR/Cas9 system. Nucleic Acids Res 44:e86

DOI

51
Strecker J, Jones S, Koopal B, Schmid-Burgk J, Zetsche B, Gao L, Makarova KS, Koonin EV, Zhang F (2019a) Engineering of CRISPR-Cas12b for human genome editing. Nat Commun 10:1–8

DOI

52
Strecker J, Ladha A, Gardner Z, Schmid-Burgk JL, Makarova KS, Koonin EV, Zhang F (2019b) RNA-guided DNA insertion with CRISPR-associated transposases. Science 365:48–53

DOI

53
Tanenbaum ME, Gilbert LA, Qi LS, Weissman JS, Vale RD (2014) A protein-tagging system for signal amplification in gene expression and fluorescence imaging. Cell 159:635–646

DOI

54
Teng F, Li J, Cui T, Xu K, Guo L, Gao Q, Feng G, Chen C, Han D, Zhou Q (2019) Enhanced mammalian genome editing by new Cas12a orthologs with optimized crRNA scaffolds. Genome Biol 20:1–6

DOI

55
Vertex (2018a) A safety and efficacy study evaluating CTX001 in subjects with severe sickle cell disease. ClinicalTrial.gov Identi fier: NCT03745287. (clinicaltrials.gov/ct2/show/NCT03745287)

56
Vertex (2018b) A safety and efficacy study evaluating CTX001 in subjects with transfusion-dependent β-thalassemia. ClinicalTrial. gov Identifier: NCT03655678. (clinicaltrials.gov/ct2/show/ NCT03655678)

57
Wang S, Su JH, Zhang F, Zhuang X (2016) An RNA-aptamer-based two-color CRISPR labeling system. Sci Rep 6:26857

DOI

58
Wang B, Zhu L, Zhao B, Zhao Y, Xie Y, Zheng Z, Li Y, Sun J, Wang H (2019a) Development of a haploid-inducer mediated genome editing system for accelerating maize breeding. Mol Plant 12:597–602

DOI

59
Wang C, Liu Q, Shen Y, Hua Y, Wang J, Lin J, Wu M, Sun T, Cheng Z, Mercier R (2019b) Clonal seeds from hybrid rice by simultaneous genome engineering of meiosis and fertilization genes. Nat Biotechnol 37:283–286

DOI

60
Wang H, Nakamura M, Abbott TR, Zhao D, Luo K, Yu C, Nguyen CM, Lo A, Daley TP, La Russa M (2019c) CRISPR-mediated live imaging of genome editing and transcription. Science 365:1301–1305

DOI

61
Wu X, Mao S, Ying Y, Krueger CJ, Chen AK (2019) Progress and Challenges for Live-cell Imaging of Genomic Loci Using CRISPR based Platforms. Genom Proteom Bioinform 17:119–128

DOI

62
Xue Y, Acar M (2018) Live-cell imaging of chromatin condensation dynamics by CRISPR. iScience 4:216–235

DOI

63
Yan S, Tu Z, Liu Z, Fan N, Yang H, Yang S, Yang W, Zhao Y, Ouyang Z, Lai C (2018) A Huntingtin Knockin PIG model recapitulates features of selective neurodegeneration in Huntington’s disease. Cell 173(989–1002):e1013

DOI

64
Yan WX, Hunnewell P, Alfonse LE, Carte JM, Keston-Smith E, Sothiselvam S, Garrity AJ, Chong S, Makarova KS, Koonin EV (2019) Functionally diverse type V CRISPR-Cas systems. Science 363:88–91

DOI

65
Yang LZ, Wang Y, Li SQ, Yao RW, Luan PF, Wu H, Carmichael GG, Chen LL (2019) Dynamic imaging of RNA in living cells by CRISPR-Cas13 systems. Mol Cell 76(981–997):e987

DOI

66
Ye H, Rong Z, Lin Y (2017) Live cell imaging of genomic loci using dCas9-SunTag system and a bright fluorescent protein. Protein Cell 8:853–855

DOI

67
Zhang F (2019) Development of CRISPR-Cas systems for genome editing and beyond. Q Rev Biophys 52:e6

DOI

68
Zhang W, Wan H, Feng G, Qu J, Wang J, Jing Y, Ren R, Liu Z, Zhang L, Chen Z (2018) SIRT6 deficiency results in developmental retardation in cynomolgus monkeys. Nature 560:661–665

DOI

69
Zhang R, Liu J, Chai Z, Chen S, Bai Y, Zong Y, Chen K, Li J, Jiang L, Gao C (2019) Generation of herbicide tolerance traits and a new selectable marker in wheat using base editing. Nat Plants 5:480–485

DOI

70
Zhong Y, Liu C, Qi X, Jiao Y, Wang D, Wang Y, Liu Z, Chen C, Chen B, Tian X (2019) Mutation of ZmDMP enhances haploid induction in maize. Nat Plants 5:575–580

DOI

71
Zhou Y, Wang P, Tian F, Gao G, Huang L, Wei W, Xie XS (2017) Painting a specific chromosome with CRISPR/Cas9 for live-cell imaging. Cell Res 27:298–301

DOI

72
Zhou C, Sun Y, Yan R, Liu Y, Zuo E, Gu C, Han L, Wei Y, Hu X, Zeng R (2019a) Off-target RNA mutation induced by DNA base editing and its elimination by mutagenesis. Nature 571:275–278

DOI

73
Zhou Y, Sharma J, Ke Q, Landman R, Yuan JL, Chen H, Hayden DS, Fisher JW, Jiang MQ, Menegas W (2019b) Atypical behaviour and connectivity in SHANK3-mutant macaques. Nature 570:326–331

DOI

74
Zuo E, Sun Y, Wei W, Yuan T, Ying W, Sun H, Yuan L, Steinmetz LM, Li Y, Yang H (2019) Cytosine base editor generates substantial off-target single-nucleotide variants in mouse embryos. Science 364:289

DOI

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